1IC8 | pdb_00001ic8

HEPATOCYTE NUCLEAR FACTOR 1A BOUND TO DNA : MODY3 GENE PRODUCT

• PDB DOI: https://doi.org/10.2210/pdb1IC8/pdb
• NAKB: 1IC8

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-03-30 Released: 2002-11-27 
• Deposition Author(s): Chi, Y.-I., Frantz, J.D., Oh, B.-C., Hansen, L., Dhe-Paganon, S., Shoelson, S.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.312 (Depositor) 
• R-Value Work: 
  0.254 (Depositor), 0.262 (DCC) 
• R-Value Observed: 
  0.260 (Depositor) 

Literature

Diabetes mutations delineate an atypical POU domains in HNF1-Alpha

Chi, Y.-I., Frantz, J.D., Oh, B.-C., Hansen, L., Dhe-Paganon, S., Shoelson, S.E.

(2002) Mol Cell 10: 1129-1137

• PubMed: 12453420 
• DOI: https://doi.org/10.1016/s1097-2765(02)00704-9
• Primary Citation Related Structures: 
  1IC8


• PubMed Abstract: 
  

  Mutations in Hnf-1alpha are the most common Mendelian cause of diabetes mellitus. To elucidate the molecular function of a mutational hotspot, we cocrystallized human HNF-1alpha 83-279 with a high-affinity promoter and solved the structure of the complex. Two identical protein molecules are bound to the promoter. Each contains a homeodomain and a second domain structurally similar to POU-specific domains that was not predicted on the basis of amino acid sequence. Atypical elements in both domains create a stable interface that further distinguishes HNF-1alpha from other flexible POU-homeodomain proteins. The numerous diabetes-causing mutations in HNF-1alpha thus identified a previously unrecognized POU domain which was used as a search model to identify additional POU domain proteins in sequence databases.

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Organizational Affiliation: 
• Joslin Diabetes Center, Department of Medicine, Harvard Medical School, Boston, MA 02215, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 57.86 kDa 
• Atom Count: 3,826 
• Modeled Residue Count: 385 
• Deposited Residue Count: 430 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HEPATOCYTE NUCLEAR FACTOR 1-ALPHA	C [auth A], D [auth B]	194	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P20823 (Homo sapiens) Explore P20823  Go to UniProtKB:  P20823
PHAROS:  P20823 GTEx:  ENSG00000135100

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*TP*TP*GP*GP*TP*TP*AP*AP*TP*AP*AP*TP*TP*CP*AP*CP*CP*AP*GP*A)-3'	A [auth E]	21	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*TP*CP*TP*GP*GP*TP*GP*AP*AP*TP*TP*AP*TP*TP*AP*AP*CP*CP*AP*AP*G)-3'	B [auth F]	21	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.312 (Depositor) 
• R-Value Work:  0.254 (Depositor), 0.262 (DCC) 
• R-Value Observed: 0.260 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.389	α = 90
b = 50.389	β = 90
c = 207.272	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-11-27 
Deposition Author(s): Chi, Y.-I., Frantz, J.D., Oh, B.-C., Hansen, L., Dhe-Paganon, S., Shoelson, S.E.

Revision History  

• Version 1.0: 2002-11-27
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-02-01
  Changes: Structure summary
• Version 1.4: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.5: 2024-02-07
  Changes: Data collection, Database references